[gmx-users] configure: error: cannot compute sizeof (off_t)

[Justin Kat]

Im not quite sure if this is the right place to analyze, but a bit
before the part in the config.log where it states the error of "cannot
compuete sizeof (off_t)", there is this:

configure:25048: checking size of off_t

configure:25053: /usr/local/bin/mpicc -o conftest  -O3 -fomit-frame-pointer -fin
line-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -I/usr/loc
al/include -L/usr/local/lib  conftest.c -lnsl -lm  >&5

configure:25053: $? = 0
configure:25053: ./conftest
./conftest: error while loading shared libraries: libmpi.so.0: cannot open share
d object file: No such file or directory
configure:25053: $? = 127
configure: program exited with status 127

configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.3"
| #define PACKAGE_STRING "gromacs 4.5.3"

| #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.3"

| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/

Also before this there a multiple chunks of such

configure:25019: $? = 0
configure:25019: ./conftest
./conftest: error while loading shared libraries: libmpi.so.0: cannot open share

d object file: No such file or directory
configure:25019: $? = 127
configure: program exited with status 127
configure: failed program was:
| /* confdefs.h */

parts all over the place.


It seems like I am missing some files somewhere?


On Feb 20, 2011, at 9:30 PM, Justin Kat wrote:

>* Dear experts,
*>*
*>* I am still unable to overcome this error during the configuration:
*>*
*>* configure: error: cannot compute sizeof (off_t)
*>* See `config.log' for more details.
*So what does config.log say about "cannot compute sizeof (off_t) ?"

Carsten

>*
*>* I came across this thread with the exact same setup as I have:
*>*
*>* http://lists.gromacs.org/pipermail/gmx-users/2011-February/058369.html
*>*
*>* I have tried uninstalling openmpi 1.4.4 and installing the more
stable openmpi1.4.3 but I am still experiencing the same error.
*>*
*>* ./configure --enable-mpi --program-suffix=_mpi
MPICC=/usr/local/bin/mpicc --with-fft=fftw3
*>*
*>* I have also tried to explicitly provide the path to mpicc as above
but it still gives me the same error.
*>*
*>* This may or may not be relevant but at the end of the config.log
there is also this line:
*>*
*>* configure: exit 77
*>*
*>* Does that mean anything?
*>*
*>* Any help at all is appreciated!
*>*
*>* Thanks,
*>* Justin--
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry

Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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